7Q2W | pdb_00007q2w

Mutant T91S of uridine phosphorylase from Shewanella oneidensis

PDB DOI: https://doi.org/10.2210/pdb7Q2W/pdb

Classification: TRANSFERASE
Organism(s): Shewanella oneidensis MR-1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-10-26 Released: 2022-04-06
Deposition Author(s): Polyakov, K., Safonova, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.232 (Depositor), 0.234 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Role of conformational changes of hexameric bacterial uridine phosphorylases in substrate binding

Polyakov, K.M., Mordkovich, N.N., Safonova, T.N., Antipov, A.N., Okorokova, N.A., Dorovatovskii, P.V., Veiko, V.P.

(2021) Crystallogr Rep 66: 786-790

DOI: https://doi.org/10.1134/S1063774521050199

Macromolecule Content

Total Structure Weight: 161.36 kDa
Atom Count: 11,845
Modeled Residue Count: 1,472
Deposited Residue Count: 1,506
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A [auth DDD] B [auth FFF] C [auth AAA] D [auth CCC] E [auth EEE] A [auth DDD], B [auth FFF], C [auth AAA], D [auth CCC], E [auth EEE], F [auth BBB]	251	Shewanella oneidensis MR-1	Mutation(s): 1 Gene Names: udp, SO_4133 EC: 2.4.2.3
UniProt
Find proteins for Q8E9X9 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8E9X9 Go to UniProtKB: Q8E9X9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8E9X9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URA (Subject of Investigation/LOI) Query on URA Download:Ideal Coordinates CCD File SDF format, chain I [auth FFF] MOL2 format, chain I [auth FFF] mmCIF format, chain I [auth FFF]	I [auth FFF]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Interactions Focus chain I [auth FFF] Interactions & Density Focus chain I [auth FFF]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth BBB] SDF format, chain O [auth BBB] SDF format, chain N [auth EEE] SDF format, chain L [auth AAA] SDF format, chain K [auth FFF] SDF format, chain J [auth FFF] SDF format, chain G [auth DDD] MOL2 format, chain P [auth BBB] MOL2 format, chain O [auth BBB] MOL2 format, chain N [auth EEE] MOL2 format, chain L [auth AAA] MOL2 format, chain K [auth FFF] MOL2 format, chain J [auth FFF] MOL2 format, chain G [auth DDD] mmCIF format, chain P [auth BBB] mmCIF format, chain O [auth BBB] mmCIF format, chain N [auth EEE] mmCIF format, chain L [auth AAA] mmCIF format, chain K [auth FFF] mmCIF format, chain J [auth FFF] mmCIF format, chain G [auth DDD]	G [auth DDD] J [auth FFF] K [auth FFF] L [auth AAA] N [auth EEE] G [auth DDD], J [auth FFF], K [auth FFF], L [auth AAA], N [auth EEE], O [auth BBB], P [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth DDD] Focus chain J [auth FFF] Focus chain K [auth FFF] Focus chain L [auth AAA] Focus chain N [auth EEE] Focus chain O [auth BBB] Focus chain P [auth BBB] Interactions & Density Focus chain G [auth DDD] Focus chain J [auth FFF] Focus chain K [auth FFF] Focus chain L [auth AAA] Focus chain N [auth EEE] Focus chain O [auth BBB] Focus chain P [auth BBB]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth AAA] SDF format, chain H [auth DDD] MOL2 format, chain M [auth AAA] MOL2 format, chain H [auth DDD] mmCIF format, chain M [auth AAA] mmCIF format, chain H [auth DDD]	H [auth DDD], M [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth DDD] Focus chain M [auth AAA] Interactions & Density Focus chain H [auth DDD] Focus chain M [auth AAA]